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Merge pull request #1149 from broadinstitute/ldg_fixCGPbugForAndrea 

Fix bug when using --ignoreInputSamples
This commit is contained in:
ldgauthier 2015-09-04 11:17:15 -04:00
parent a8851e6763 4769ef8dad
commit cad81a6181
1 changed files with 4 additions and 1 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
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@ -93,7 +93,10 @@ public class PosteriorLikelihoodsUtils {
} }
//add zero allele counts for any reference alleles not seen in priors (if applicable) //add zero allele counts for any reference alleles not seen in priors (if applicable)
totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources); int existingRefCounts = 0;
if (totalAlleleCounts.containsKey(vc1.getReference()))
existingRefCounts += totalAlleleCounts.get(vc1.getReference());
totalAlleleCounts.put(vc1.getReference(),existingRefCounts+numRefSamplesFromMissingResources);
} }
// now extract the counts of the alleles present within vc1, and in order // now extract the counts of the alleles present within vc1, and in order